A lot of things had changed in that long lapse of time that seemed sometimes to flow ever so slowly, like it was fully ignorant of the pain and suffering it was causing. At first he tried to move on with his life, but he had found that he had nothing of it left. His life and all his time had been devoted solely to Sherlock and with him gone he had no other occupation to busy his already suffering mind and tarnished heart. Whenever he did attempt to do so, he found everything reminded him of him. The presence of one thing and the lack of another, all seemed to further tear his heart apart as if with wild and ferocious teeth. Even the people he could not tolerate, simply because they knew. They knew what had happened and they had been there and they knew how he suffered and the way they stared. The way they looked at him with their piercing eyes full of all the mourning and grief he had wanted to avoid so desperately, but which seemed to chase after him everywhere he went. Their eyes bored holes into his body and their words cut at his skin like razor blades. Their handshakes and pats on the back seemed like they were breaking every bone in his body and even when he walked away hurriedly, leaving them with the simple expression of 'I can't.', he could feel their compassionate stares drilling into his back and he just couldn't.
He had wanted to move on but he just couldn't.
So he slowly drifted away into the ocean of forgetfulness. He wanted to forget what happened and to wake, washed up on the shore of another reality, one where no one knew his name, nor his past, nor the horrors that had driven him there. So he did everything in his power to accomplish that. He moved out of the apartment. Mrs. Hudson's mere presence evoked in him too many fond and painful memories.
Then there were the things. The entire messy apartment was filled with Sherlock's things and as he rummaged through them he could feel his heart pounding in his chest, like it was trying to jump straight out of his ribcage with the sheer mixture of emotions.
He left the apartment. He found a job. And he had tried to cut off any and all ties binding him to his past life. It was difficult, but humans prove to be less persistent than one might think, when dealing with another's personal problems. And so with the final ropes loosened, he was allowed to drift off. And he did. He lived in a small apartment, as far away from 221b, but still close enough to anything he needed. He worked at his nine to five job and he even attempted some vague socializing with his colleagues, although all that time spent with Sherlock had somewhat hindered his social skills.
During his free time he read and took up hobbies. Anything and everything to keep his mind occupied and away from "it".
And it worked.
Not once had he shed a single tear, not since that last one that he allowed to fall on the ground under Sherlock's tombstone. He had been, as experts would call it "coping by not coping", or as he would call it, attempting to survive without being driven stark raving mad.
Only at night he sometimes let his thoughts wonder freely and sometimes it all seemed to him like a lucid dream. He asked himself, if it had really happened. Perhaps he had dreamed it all and his real life had always been here, in the small, bleak apartment he quite disliked, but could only afford, the job he most definitely not enjoyed and the friends he had failed to make. No. It had not been a lucid dream, it had been quite real and it had quite really managed to ruin him in every sense of the word. Still he imagined it and imagined what his life would have been like, had he never been introduced to Sherlock. He succeeded in convincing his mind that it would have been much better for him, had he perhaps not gone out for a walk in the park on that accursed day. But in his heart he knew it was not true. Meeting Sherlock had been the best thing to ever happen in his life and quite probably the last. And whatever true happiness, however short lived, was worth cherishing, regardless of the consequences it may have brought on later. He knew this, but he kept it safely locked up in a little box. A little like Sherlock's mind palace, he from time to time thought and let out a small hint of a smile. But not like it at all really. Just a place in his mind where he could keep his grief, his sorrow, his emotions, his memories, his love and ultimately his whole heart.

It had been three years and for John Hamish Watson much had changed. Not necessarily for the better of his heart and soul, but definitely for the better of his mental health.

So it was, that he had settled into a routine. Humans, who have experienced something thoroughly mind blowingly extraordinary, seldom forget the occurrence entirely, but they can, with will and patience however, succeed in pushing it out of their memory, so that it does not constantly linger. And that was precisely what he had done. He had settled into a mundane, dull and quite frankly pretty boring and ordinary routine.
Nothing ever happened to him. Not any more.
So imagine the surprise, if you will, on John's tired and overworked face, when he arrived to the door of his flat, only to stop as if he had been struck by lightning. His hand, clasping the key, frozen mid-air on the way to the lock.
He stood there, completely petrified and listened. Listened to hear what had stopped him in the first place, once more. A high-pitched note from a violin. A tone that could belong to any instrument of similar build, that could have come from any flat and that was, for all he knew, simply in his mind. But at that very moment, in his brain, buried deep, within the box, locked away under all the grief and sorrow, his heart seemed to beat once more. It jumped, and with it came the hope, the expectation and the flood of emotions. He stood there, completely motionless for what could have been a good ten minutes. After which time, he had successfully told himself, it was just a wild fantasy, a useless and ludicrous thought. Accepting that the reality of this was in fact, quite impossible and extremely improbable, he regained his composure and slid the key into the latch. A simple, mechanic movement, that seemed in this particular instance to last a whole lifetime. He heard the cold, iron parts of the lock, fall into place and clasp around the key with a series of clicks, the sound of which completely fascinated him. For no particular reason, a lump had started to form in his throat and he slowly turned the handle of the door pushing it open and, as an act of habit, removed the key from the lock.
As he did so, he once again stopped. But for an altogether different reason. He loosened his hand and let the key fall to the floor, along with his bag and the groceries he had been carrying. Time once again seemed to flow painfully slow and as he started to feel a pressure building in his chest, he realized he had in fact, stopped breathing. He felt as though his bone structure was going to disintegrate completely and he broke out in a cold sweat.
The very connections that connected his brain to the nerves in his eyes, seemed to him to be broken, for his brain could not even begin to process what his eyes were beholding.

Because in front of him, at the end of the short entrance hall, in front of the window that faced the main street and was directly in front of the front door, next to which John stood, dumbfounded. In front of the sitting chair John used for his reading, stood, violin loosely hanging from his hand, bow placed on the sofa, Sherlock Holmes himself.

For a moment, that seemed like a year, because as we had mentioned before, time seemed to flow painfully slowly, they just stood there. John looking at him, feeling all of his bodily functions failing. His heart telling him this was real, this was happening, threatening to set forth and incredible mass of emotions, all the while his mind was attempting to rationalize it and either way he formed the equation, he saw it was, by all the laws of nature and science, completely impossible.
Sherlock also stood there. His same, calm and composed self. But there was something about him, a certain tinge in his demeanor that indicated, he was also quite unsure of his presence here. His manner was not altogether the entitled, confident one John had been accustomed to, it was a slightly humbler, more tender version of Sherlock, one that many believed did not exist and few had ever truly seen.

All of a sudden, apparently feeling that enough mental analysis had gone by and perhaps feeling the need to affirm that he was in fact standing here, that he was not an illusion, a mirage brought on by a tortured and troubled mind, Sherlock broke the silence:

"Hello, John."

Something seemed to snap in John at that very moment. It felt like a strong pang in his chest and if you had asked him, he would have told you he thought it had been audible from a 5 block radius. However it felt and did or did not sound like, he would not, for the life of him be able to completely encompass the wave of mixed sensations that flowed through his body at that time, for the English language I'm afraid, does not have a broad enough vocabulary to be able to do those emotions justice.
All he was able to do, whilst feeling like he was going to snap at the weight of the pain, the joy, the anger, the sadness, the frustration and the intensity of the recurring event, was fall onto his knees and let forth the flood of tears that he had been holding back all of these years.
He cried for the moment Sherlock called him, for the surprise when he saw him fall, the moment when he saw his mangled body lying on the pavement in front of St. Bartholomew's Hospital. All those nights when he thought about him, for the funeral, the grief, the mourning all wanted to happen at once and John had not the force of will to hold it at bay. His joy way equaled by his anger, his bewilderment by his frustration and as he slowly sinked with his head onto the tiled floor, bringing his knees up to his chest, he could only see one word, printed out at the back of his brain in large block letters:

WHY

''why? why?! WHY WHY WHY WHY?!" He lifted his head up and looked up at the man he still had a hard time believing was there and screamed. Sherlock had, from the looks of things been caught entirely by surprise, for this hadn't been the reaction he had expected. Although, having combined the extraordinary circumstances and the sheer strangeness of this particular event, predicting any kind of reaction is something that would have been beyond anyone's capabilities, let alone the ones of a "high functioning sociopath".
He stared at him in blank amazement, a wave of emotions he did not know he possessed coming forth, flowing from his eyes in the shape of tears he did not know he was capable of crying. Struggling to move his feet forward he advanced, first slowly, then rapidly until he was kneeling at John's side, silently hugging him, clasping him tightly to his chest as if trying to make up for all the time lost.

Of all the emotions predominating in John's body, the one that expressed itself more firmly at the moment was sheer anger. "WHY?! WHY?! WHY NOW THEN SHERLOCK TELL ME WHY!" he screamed and began to pound into Sherlock's chest. Why now, why at all, why did he leave, why for three years, why didn't he tell me his plan, why show up now, why, why why. It was all that sounded in John's brain and he shouted and shouted at Sherlock hoping to at least get a response. A logical, coherent response that would be to his placid, normal mind too out of reach to derive for himself, but that would, coming from Sherlock's mouth, make perfect sense and soothe his frustration.
He received no such response.
Instead Sherlock just quietly sobbed, clasping John even more tightly towards him, to stop the punching, to make him know and understand that he was back, he was here and he would never leave again.

They stayed like this for god knows how long and after a while John calmed down. Having finally let out his anger, now only confusion and some form of strange, blissful happiness remained. Exhausted, both physically and mentally, he let himself fall limply into Sherlock's arms.
The tears had ceased to flow, not so much because the impulse to cry had been suppressed, but more because their bodies seemed to have exhausted their lifetime supply.
In this tight embrace they remained silently for some time, not saying anything, merely taking in each other's presence, the feel of their bodies together, still not quite fully grasping the reality of the situation.

After some time, Sherlock said the only thing that he needed to say at that particular moment:

"I'm sorry John."

John said nothing, merely tightened his embrace and made a sound that seemed to emanate straight from his heart, sending chills through Sherlock's spine and, that translated into words meant, at least to Sherlock's ears a mixture of "I forgive you", "Thank god you're back", "I love you" and "Never again".

It was all either of them needed really and they allowed each other to drift off to sleep in each other's embrace right there in the hall, not moving to the bedroom for risk of breaking contact for a single second. After all, tomorrow would be a new day and they could then begin to rebuild their new life once more.